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	<title>Assembly Options</title>
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	The default assembly parameters have been tuned on a large variety of libraries. See online documentation
	for more detailed information on the assembly process. Note that TCW can assemble Sanger and 454 raw reads, 
	as well as existing transcript sets, but cannot assemble raw Illumina reads or similar datasets.
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					Assemble
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			<td  valign="top">Clique</td>
			<td>
				Determines which overlaps are accepted from the clique MegaBLAST output.<br>
				Minimal overlap: minimum matching bases allowed.<br>
				Minimal %identity: minimum identity of the match.<br>
				Maximal overhang: maximum number of non-matching bases attached to the putative joining region.
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			<td  valign="top">Clique Blast Eval</td>
			<td>E-value for MegaBLAST used to form cliques.</td>
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			<td  valign="top">Clique Blast Parameters</td>
			<td>Additional parameters for MegaBLAST used to form cliques.</td>
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			<td  valign="top">Self Join</td>
			<td>
				Determines which MegaBLAST results are accepted for overlapping 5' and 3' mate pairs.
				See description under "Clique" above.			
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			<td  valign="top">Bury Blast Eval</td>
			<td>E-value for the initial bury blast. </td>
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			<td  valign="top">Bury Blast Identity</td>
			<td>%Identity (-p) for the initial bury blast.</td>
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			<td  valign="top">Bury Blast Params</td>
			<td>Additional parameters for the initial bury blast.</td>
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			<td valign="top">CAP Args</td>
			<td>Parameters for running cap3 (also used for assembling cliques).</td>
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			<td valign="top">TC Blast Eval</td>
			<td>E-value for blast overlaps during contig merge stages.</td>
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			<td valign="top">TC Blast Params</td>
			<td>Additional parameters for blast overlaps during contig merge stages.</td>
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			<td valign="top">User EST Self Blast</td>
			<td>Path to the initial bury blast output file, if done outside of PAVE.</td>
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			<td valign="top">TC#N Table</td>
			<td>
				Parameters for loading MegaBLAST results for 
				Nth contig merge round. See description under "Clique" above.
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